Affiliations
by tridget
Summary: John Sheppard tries to cope with the fallout from the events of "Remnants."


**Author's Notes: **Thank you to my awesome beta reader, **wildcat88**, especially for making sure I said what I meant. All mistakes are my own. Spoilers for "Remnants," and a small one for "Sanctuary."

* * *

**Affiliations**

John had made a pact with himself. The pact was necessary to preserve his dignity at the times when it was most in need of preserving. He'd promised himself that he would count slowly to thirty any time he had the urge to ask to get out of the infirmary. He'd convinced himself that it made him look less desperate.

John began his snail-paced count as Keller held his left arm in a firm but gentle grasp, manipulating it one way and then another.

"Can I lose this?" John blurted, jiggling the IV line around as he waved his other arm. _Crap_. He hadn't even reached twenty yet. _It must be the drugs_, he thought.

"We'll see…" Keller continued her examination.

John tried to school his expression into that of a model patient. He was sure that his eyes ruined the effect, darting towards the exit against his will. Technically, he told himself, he hadn't broken his contract. He hadn't actually asked to get out of the infirmary. He was still good. But he forced himself to start the count from the beginning to compensate for his slip-up.

"And you're not in any pain at the moment?" Keller asked.

"No. None at all. My arm feels great." John winced, suspecting his reply had been way too enthusiastic. "Can I get outta here now?" _For Chrissakes, John, you didn't even make it to ten this time_. It was definitely the drugs.

Keller pursed her lips and frowned as she studied John. "Colonel, when Rodney called for medical assistance last night, he said he found you, and I quote, 'lying on the floor, screaming and writhing in agony.'"

John twisted his face and made a dismissive gesture with his right hand, tangling his fingers in the IV tubing. "McKay exaggerates."

"Rodney does have a tendency to do that." Keller smiled — sort of a dreamy, fond kind of smile.

John smiled back. Victory was at hand.

Picking up her datapad, Keller scanned through the medical notes. "The night duty nurse, Marie, described you as being in 'excruciating pain…'"

That one was going to be a bit harder to argue. "Okay, it hurt. Quite a lot, if you want to know the truth." _Like that admission is gonna help your case_. "But I wouldn't use the word 'excruciating' to describe it." _Better_.

"Uh huh." Keller looked unconvinced as she continued to scroll through John's chart. She placed her finger next to an entry. "Doctor Cole asked you to rate the pain on a scale of one to ten. She reported that your answer was, and again I quote, 'It's a friggin' twelve.'"

The way Keller said 'friggin' twelve' was so polite and so serious and so damned funny. John laughed. "I think the 'twelve' part threw her for a loop," he offered. Then, realizing he was fouling up his chances of going back to his quarters, he leaned back and let his head thump onto the pillow. He was sure the drugs had been much more fun when he'd had his wisdom teeth extracted. Of course, he didn't have his reputation as military leader of Atlantis to worry about back then.

"You told Doctor Cole you'd injured your arm when you were with the Sekkari," Keller pressed on, "but my notes from last week only indicate bruising to the right side of your chest and soft tissue damage to your right arm and shoulder from your tumble over the cliff. You didn't mention any injury to your left arm then."

John shrugged. "Musta forgot."

"Well, now that you've remembered and all, maybe you'd like to fill me in."

John had the feeling that underneath her sweet demeanor, Keller was circling him like a shark. "I don't remember the specific details. The part before the cliff was confusing, you know. I might've twisted it or something."

"Or something…" Keller repeated, her dissatisfaction with his answer obvious.

_Don't say anything. Don't open your mouth and stick your foot in any further than you already have_ . "The Sekkari were screwing with my mind. You can't get a real injury during an imaginary event, can you?" _Way to go, John_.

Keller frowned. "In this case, I'm not so sure. Rodney and Mr. Woolsey were going about their regular duties during their time with the Sekkari. If they'd had a real accident during that time…presumably they would have experienced a real injury. If the injury had been part of the experience with the Sekkari…I'm not sure…" She skimmed John's chart again. "In any case, the pain you were experiencing seems to have been very real."

"Some people have phantom pains when they lose a limb, right? The pain's real but the arm or leg isn't." _It wasn't necessary to bring that up, you know_.

"Yeah, that can happen, but I'm not sure how that relates…" Keller narrowed her eyes, studying John as though close scrutiny might reveal information that the scanner had missed, information that would sort this whole mess out.

John flexed his elbow and looked at his hand. Unscathed. He lifted his head, flinching when sunlight flashed off the blade of the machete. His heart began to hammer so hard it almost hurt and his lungs worked overtime, pulling in oxygen in short, frantic heaves. John bit down on his lip, bracing for the inevitable as steel sliced the air.

"Colonel?"

This time there was no pain. But there was still the sound of metal squelching through flesh, the snap of shattered bone, the dull thump as his hand hit the ground, blood gushing everywhere…

"Colonel!" Keller took hold of John's arm again.

John sucked in a sharp breath and blinked, trying to focus on Keller. Her fingers were cool on his wrist as she took his pulse. His wrist. His hand. Still attached. And shaking badly.

"Does your arm hurt again?"

"N-no." John licked his dry lips. "I…uh…sorry." He swallowed and closed his eyes. "I think the medication's making me feel kinda sick." _Yeah, that or the memory of having your hand chopped off_.

"Oh. Well, it does have that effect sometimes. I can get you something for the—"

"No!" John's eyes flew open again. "I…I just want to have this IV taken out, go back to my quarters, and get some sleep." He scrubbed his hands over his face, feeling fatigue hit him all at once. "It's been a long night."

Keller sighed. "Tell you what. I'll remove the IV. You try to get a couple more hours of sleep here while I wait for all the test results to come back. If you have no more pain and the results are normal, I'll let you go then."

As much as John wanted to go back to his room, he wasn't sure he had the energy to make it on his own now. "Deal." _Two hours, John. Don't mess it up between now and then_.

Keller removed the IV. "And…um…maybe the results will help clarify for you what was real and what wasn't…"

John nodded. "Thanks, Doc." He scrunched down on the bed and curled up, finding Keller's suggestion oddly reassuring.

Keller pulled a blanket over him. "Get some sleep." She patted his good shoulder.

The blanket was warm and the weight of Keller's hand solid and real as John drifted off. The sensations fought off the nagging fear that maybe he was still trapped in an illusion. "This is the nice part of bein' in the infirm'ry." _I did_ not _just say that_.

Keller let out a funny-sounding huff that might've been a cut-off chuckle.

~~~~oooo~~~~

Keller looked up from the results of the scans and various other tests that probably hadn't been designed with the patient who imagined their arm cut off in mind. "Everything's within the normal range."

"That's good." John felt as though a weight had been lifted. But that was ridiculous because he'd known his arm was fine. That was obvious, wasn't it? Maybe it had taken his brain a while to catch up with the reality.

"I know it doesn't explain what happened last night, but maybe it'll help you sort out some of the confusion. I still want you to take it easy."

"I will." John hopped off the bed.

Keller scowled.

Okay, so maybe springing off the bed had made his promise seem less convincing. _She's probably not too impressed with the way you staggered and grabbed the edge of the bed to steady yourself either_.

"You're off duty until tomorrow. I want you to rest in your quarters. After that, you're still on light duty because of the injury to your right side. I'll see you again on Thursday."

"I'm just going to get some lunch first. I'm starving."

Keller narrowed her eyes. "I can arrange to have lunch brought to your quarters. You haven't quite recovered—"

"My arm's okay. The tests even said so." John lifted his arm and waggled his fingers in the air.

"I meant from the painkillers."

"What? I feel good now. Great, actually."

Keller's mouth tightened and her brows knit together. "Which is my point exactly."

John pulled himself up, attempting to look as stable as he possibly could. "Lunch. With my team." He needed to prove something though he wasn't quite sure what. Maybe he needed to prove that he was okay, but he wasn't quite sure who needed the proof.

"Then you'll go to your quarters?"

"Then I'll go to my quarters — right after I stop by Woolsey's office because I'm supposed to have a meeting with him today." _Could've done without adding that part_.

Keller grimaced. "Sorry to hear that."

"Why does everyone assume I'm in trouble? Ronon offered me his digital voice recorder so I could get my paperwork caught up, but I'm not even behind on paperwork." _Not by much…and nothing really important_.

"Well, whatever it is you're asked to explain, I'm sure you'll do a fine job." Keller gave her most reassuring smile.

"Thanks. I think."

"Yeah… Anyway, Mr. Woolsey knows you were brought in here last night. I'll call him and—"

"Look, you told me I had to rest and take it easy right?"

Keller hesitated. "Why do I feel like I'm walking into a trap?"

John waited.

"Okay, yes, you have to rest," Keller folded her arms.

"So how can I possibly rest knowing that I have this meeting hanging over my head?"

Keller shook her head. "Did Doctor Beckett ever mention to you that you're a really difficult patient?"

"More times than I can count."

John smiled as he left the infirmary, but it wasn't just because of the drugs. It was having a doctor who'd understood what he needed and who'd offered his mind the first bit of relief he'd had from the fallout of that goddamned trip.

~~~~oooo~~~~

John knocked on the frame of the door-less entryway to Woolsey's office.

Woolsey looked up from the work on his desk. "Ah, Colonel Sheppard. I heard about your admission to the infirmary last night. Are you sure you're—"

"I'm fine. It was just…from last week….a…uh…muscle spasm." _Can you still call it that when it was your brain that seized up_?

"Well…I'm glad to see that you've been released. Please," Woolsey gestured to the armchairs, "make yourself comfortable."

John eased himself into a square seat that was anything but comfortable.

Woolsey stood up, straightening his already crease-free jacket. "Life in the Pegasus Galaxy presents us with unique challenges," he began as he walked out from behind his desk. He paused and then nodded, seeming satisfied with his opening sentence. Heading towards the armchair opposite John, Woolsey continued, "We are all called upon to deal with these challenges in our own way and to the best of our ability." He sat down, fixing John with a pointed stare.

_Dealing with challenges. So that's what this meeting's about_. "Look, I know that…thing on the east pier got a little out of hand. It-it probably sounds worse in the retelling." _Hard to imagine that fiasco could be made to sound worse than it already was_.

Woolsey frowned.

"It won't happen again."

Woolsey continued to frown. "I don't recall receiving any information about a…'thing' on the east pier."

"Oh." _Well done, John. Let's see you go a couple of rounds with a Wraith queen hell bent on extracting information now_.

"Is this something with which I should concern myself?"

"No. Uh…no. It's been…dealt with." _Just a little bit of damage left to fix up_.

"Fine. Let's move on then. Colonel, I wanted to discuss your report on your encounter with the Sekkari."

_Crap. Might've been better to discuss the thing on the pier after all_. "My report? What about it?"

"It's somewhat…thin. I believe it requires additional details."

John narrowed his eyes. "What sort of details?"

Woolsey removed his glasses, pulled out a cloth from one of his pockets and polished the lenses. "Your report says very little about your interaction with the Sekkari, about the form it took, about the situations you encountered, about…"

"I'm sure my report said that the AI kept me occupied. I'm sure it said that I was given a scenario in which I was asked to assist in an invasion of Atlantis. I refused. End of story."

"Is it?" Woolsey replaced his glasses and scrutinized John.

"It is."

"Colonel, the fact is that we were compromised by an alien entity. We still have to hope that this one will not pose a threat to Atlantis at some point in the future. And the next aliens we encounter may just as easily be hostile. We must use every tool at our disposal to prepare ourselves."

"I agree." John wished that he didn't. He would have liked a point to argue, something to get hung up on, some way to get take control over the direction of the meeting. Keller was right. He should have rescheduled. On the other hand, he couldn't really blame the situation on the medication. The remains of the buzz from the drug had evaporated the second the Sekkari had been mentioned.

Woolsey's face tightened. "I realize that our individual experiences were personal…perhaps even embarrassing. But as military leader you must know that—"

"As military leader, I know how to write my own damned reports." John's retort was too loud. And a room without a door was a bad place for an office. _Congratulations. Now the whole Gateroom knows that you can write your own reports_.

Woolsey's eyes widened at John's declaration. He waited a minute before speaking again. "Vanessa…Doctor Conrad…The AI alluded to your less than pleasant experience. You made a reference to it in the debriefing, but I didn't pursue it, thinking that you might require some time to sort through the events. I had anticipated that more information would appear in your report." He hesitated. "It's not a secret that Doctor McKay's desire for adulation was used to manipulate him. The Sekkari also exploited…uh…shall we say…my desire for…affiliation."

One of John's eyebrows quirked. "A-affiliation… You're desire for…?" He cleared his throat.

"Yes." Woolsey squared his chin as though bracing himself to see this conversation through, while his face turned several shades of red.

John leaned forward, his voice low as he glanced around, making sure no one was in earshot. "You're not trying to say that you, ah…" he locked his fingers together "that the two of you…affiliated?"

"No. Oh, no." Woolsey gave a tight, vigorous shake of his head. "Nothing like that."

"Good. That's good." John sat back, shoving aside unwanted images of Woolsey having some sort of glowing activity with an ephemeral alien. "Good, because I speak from experience when I say you _don't_ want to have to put that in a report." He cringed as soon as the words left his mouth, wishing it were possible to press the rewind button on the conversation. Maybe the Sekkari hadn't given him back full control of his mind. That had to be it. That could explain everything — his arm last night, his ill-planned responses. _Or maybe they did and you're just not managing as well as you thought you were…_ John sighed and massaged his left arm, feeling a tendril of discomfort wind its way towards his elbow.

Woolsey was still talking. "I also think it is important for you to specify what characteristic was taken advantage of."

"I beg your pardon?"

Woolsey studied the arm of his chair for a minute. "You didn't mention what personal trait became a vulnerability."

"It won't happen again."

"I can accept that answer as sufficient with respect to a 'thing' on a pier. However, with respect to the security of—"

"Kolya. It was Kolya," John blurted, taken aback at how rough his voice sounded. He squeezed his left arm, trying to block the ache. His arm was fine. He was fine.

Woolsey's eyebrows shot up. "That must have been very difficult."

John took in Woolsey's look of sincere concern before turning away. "I can handle it." _Like you're handling it now_?

"Your ability to handle it is not in question. What is under scrutiny are the tactics that may be used against us and how we can best protect our city."

"Protect our city," John muttered to himself. That was something he _could_ discuss — something he _had_ to discuss. "He was going to steal the jumper. He was planning to use my ATA gene to activate the jumper to invade Atlantis." The words tumbled out in a rush before John could stop them. With his right arm, he cradled his throbbing left one against his stomach.

"And you refused to assist in the invasion?"

"Of course."

"And then?"

"He tried a bit of…physical persuasion. Didn't work." John sucked in a breath through his teeth as a white hot spike of pain burned through his wrist and seared its way towards his shoulder.

"Colonel, are you alright?"

"He cut off my hand." The words came out abrupt and hard.

Woolsey started. Then his face paled as the horror of the revelation sunk in. "My God…"

"It wasn't real." _Your arm's fine. There's nothing wrong with it. Keller said so. The tests said so_. John hung on to that tangible bit of reassurance. _Kolya's dead. Your arm's fine. Atlantis is fine_. The pain began to slither away, first to a barely tolerable ache and then it worked its way down to a vague tingle. "It wasn't real," he repeated.

"I know. But I also know how completely convincing the manifestations—"

"It's over."

Woolsey bowed his head for a moment. "Colonel, I am truly sorry that we were…that _I_ was unaware of your predicament and that I was here, caught up in my own frivolous fantasy while you were enduring your horrific scenario on the mainland. I should have suspected—"

"It's not your fault."

"But still…"

"Yeah, well, don't feel too bad because apparently my illusion was of my own choosing, too."

"Surely not…"

"Actually, I-I'm not sure what part of their explanation to believe. 'My mind manifesting my darkest fears…'" John's voice took on a mocking tone as he relayed the words spoken by the AI. _Might've gone a little too far on the self-disclosure there_.

"I see." Woolsey nodded. "Or perhaps it would be more correct to say I am beginning to understand – the burden of command – the responsibility for so many lives – each casualty no longer an acceptable risk on a piece of paper. From what I have seen in the months I've been here, I don't find it surprising that your greatest fear would be that of being forced into the service of the enemy. It is a credit to your leadership that the issue which was of greatest concern to you and most likely to divert your attention was the safety of Atlantis and its people."

John felt another weight lift from his shoulders. When Woolsey put it that way, it made John feel a little less screwed-up than he'd thought he might be. _There's still the bit about torturing yourself every day_. John felt his face flush. He wasn't quite sure why that bit of exposure by the alien was so humiliating, why that phrase had haunted him for the last week. Maybe because it was true. He couldn't brush it off by saying it wasn't real. It was a weakness and John hated appearing weak. Maybe it bothered him so much because he'd thought he kept his tendency toward self-recrimination hidden and he just realized that it hadn't been as well-concealed as he'd thought – not from the Sekkari and probably not from his friends either. The architect of his own self-deception. He didn't know whether to be grateful, or pissed off, or embarrassed that people had played along with his charade. And he sure as hell didn't know what he was supposed to do about it now.

"…so I appreciate your candidness today. Thank you." Woolsey concluded.

"What?" The meeting was over? That was it? "I mean…you're welcome. I'll…uh…I'll see what I can do about adding a few details to my report." John pulled himself up out of the chair.

"Not quite so fast…"

John _knew_ there had to be a catch.

"Doctor Keller also told me you're off duty for the rest of the day. So, the report can wait a day."

"Oh… Yeah. Musta forgot."

"Yes, she said that you might."

John gave a wry smile. "Can't get much past her."

Woolsey almost smiled back before his expression became one of concern again. "Tell me, Colonel, was the prospect of meeting with me really so bad that you had to get it over with?"

"Did Keller tell you that, too?" John felt a flash of irritation at just how much information Keller seemed to have passed on.

"No, she didn't."

"Oh." John thought for a moment. "Let's just say that reality was a bit different from what I'd imagined."

Woolsey tapped his earpiece, listening for a moment. He held up one hand, signaling John to wait before leaving the room. "Thank you…_Chuck_." Woolsey pronounced the name carefully. "Colonel, I just received word that the Apollo has reached its destination and placed the Sekkari carrier on its new home world."

"That's good. Glad to hear that." John figured he might be coping a bit better already because he'd managed to say the right thing when what he really thought was that he didn't give a rat's ass about the Sekkari.

John reached the entranceway to Woolsey's office and then pivoted back to face the man. "You know, on Friday nights when we're not offworld, my team and I usually watch a movie or two. Our friends are always welcome to join us."

"That sounds like a good idea. It certainly sounds like it might be preferable to a 'thing' on the pier." Woolsey appeared serious as always, but there was a twinkle of amusement in his eyes.

John scrubbed one hand over the back of his hair. "I meant that to be like an invitation."

"Oh. Thank you, but I…" Woolsey hesitated. "You know several months ago I would have turned down that offer. I'm not sure why, but I would have. Perhaps one Friday I might…" He took a deep breath. "On second thought, I _will_ join you this Friday."

"Good. And um…"

"Yes?"

John shook his head. "Nothing. Look forward to seeing you then." He'd been going to tell Woolsey to wear something more casual than a suit and tie, but changed his mind. It was one thing to encourage someone to make a few friends; it was another thing entirely to ask them to change who they were.

John jammed his hands in his pockets and headed for his room. Logically, he knew he should extend the same courtesy to himself, but it just wasn't that easy. Damn the Sekkari. _You're going to blame the Sekkari for what was inside your head? Although it might be a nice change from blaming yourself…_

By the time John reached his room, he had a headache and he was more than ready for the prescribed rest. Not even bothering to remove his boots, John flopped down on his bed and tossed one arm across his face. The fabric of his black wristband brushed across his skin, his daily reminder of lives that had been lost and his insurance that they'd never be forgotten. No, he was never going to change that.

But there was one thing that had changed since he first put that swathe of fabric around his wrist. He had his friends and family on Atlantis. He had a team. That was the thing the Sekkari missed. Regardless of how much personal responsibility he shouldered, he had people who helped ease some of the burden. That was never going to change now either. So nothing was different than it had been before the Sekkari, and maybe he didn't need to do anything about the revelations at all. He was fine. _Well, maybe not entirely fine, but you're doing better that you were yesterday and you will be fine again soon_.

John rolled over on his side and tucked his arm underneath his head, with the fleece of the black fabric pressing against his cheek, and fell into a peaceful sleep.

~~~~oooo~~~~

The End


End file.
